Contacts of the helix formed by residues 783 - 790 (chain B) in PDB entry 5YWB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 783 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782B ALA* 1.3 77.2 - - - +
784B VAL* 1.3 58.4 + - - +
785B GLU* 3.9 5.8 + - - +
786B GLU* 3.2 26.1 + - - +
787B ASN* 2.7 35.2 + - - -
820B GLN* 3.3 47.0 + - + +
821B THR 3.7 5.6 - - - -
822B GLN* 3.6 14.1 - - - +
823B ILE* 4.9 0.9 - - - -
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Residues in contact with VAL 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B THR* 1.3 71.1 - - - +
785B GLU* 1.3 66.6 + - - +
787B ASN* 3.1 7.4 + - - +
788B ILE* 3.0 46.6 + - + +
799B TYR* 5.2 3.1 - - - +
803B ILE* 5.6 0.7 - - + -
808B LEU* 5.3 0.2 - - + -
812B ILE* 3.8 33.2 - - + -
815B LEU* 5.0 3.8 - - + -
819B ASP* 4.0 13.0 - - - +
820B GLN* 4.5 1.6 - - - +
821B THR* 3.9 18.5 + - - +
823B ILE* 3.8 25.4 - - + -
830B LEU* 5.8 0.4 - - + -
838B ILE* 4.2 14.6 - - + -
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Residues in contact with GLU 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783B THR* 3.4 4.1 + - - +
784B VAL* 1.3 76.1 - - - +
786B GLU* 1.3 57.4 + - - +
788B ILE* 3.3 1.8 + - - +
789B THR* 2.9 35.7 + - - +
794B PHE* 3.5 30.2 - - + -
799B TYR* 3.5 20.5 - - + +
819B ASP* 2.9 37.7 - - - +
820B GLN* 2.4 43.3 + - + +
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Residues in contact with GLU 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780B LEU* 5.8 6.1 - - + +
782B ALA* 3.4 25.4 - - + +
783B THR* 3.2 24.8 + - - +
784B VAL 3.1 0.8 - - - -
785B GLU* 1.3 77.8 - - - +
787B ASN* 1.3 59.6 + - - +
789B THR* 3.0 8.6 + - - +
790B PHE* 3.0 29.6 + - - +
791B GLU 6.0 1.8 - - - +
794B PHE* 6.0 0.2 - - - -
1226B LYS* 5.5 5.0 + - - -
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Residues in contact with ASN 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B LEU* 3.5 7.3 - - - +
780B LEU* 2.7 52.1 + - - +
782B ALA* 3.9 10.9 + - - +
783B THR 2.7 29.7 + - - +
784B VAL* 3.1 9.4 + - - +
786B GLU* 1.3 76.3 - - - +
788B ILE* 1.3 58.6 + - - +
790B PHE* 4.4 3.3 - - - -
823B ILE* 4.3 8.6 - - + +
838B ILE* 4.4 13.2 - - + -
842B ARG* 3.2 49.9 + - - +
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Residues in contact with ILE 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B VAL* 3.0 33.2 + - + +
785B GLU 4.0 2.9 - - - +
787B ASN* 1.3 79.6 - - - +
789B THR* 1.3 61.2 + - - +
790B PHE* 4.7 0.6 - - - +
799B TYR* 4.4 17.9 - - + -
802B VAL* 4.5 5.6 - - + -
803B ILE* 3.6 28.3 - - + -
808B LEU* 4.5 7.2 - - + -
838B ILE* 4.7 10.5 - - + +
841B ALA* 3.8 38.6 - - + +
842B ARG* 4.2 9.9 - - - +
845B TYR* 3.1 33.5 - - + +
846B GLN* 5.4 0.3 - - - +
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Residues in contact with THR 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785B GLU 2.9 22.2 + - - +
786B GLU* 3.0 14.2 + - - +
788B ILE* 1.3 79.4 - - - +
790B PHE* 1.3 67.2 + - - +
791B GLU 3.5 2.7 + - - -
792B SER* 3.5 25.7 + - - +
794B PHE* 3.5 38.6 - - + -
799B TYR* 5.2 2.7 - - + -
845B TYR* 3.8 20.0 - - + +
846B GLN* 2.8 24.8 + - - -
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Residues in contact with PHE 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778B TRP* 4.6 4.3 - + - -
780B LEU* 4.0 28.3 - - + -
786B GLU 3.0 11.2 + - - -
787B ASN 4.4 2.9 - - - +
789B THR* 1.3 82.3 + - - +
791B GLU* 1.3 64.8 + - + +
792B SER 3.0 5.8 + - - -
842B ARG* 3.5 43.7 - - + -
846B GLN* 3.1 18.6 + - + +
1213B THR* 4.7 14.6 - - + -
1214B ILE* 4.7 5.8 - - + -
1217B PHE* 4.5 17.9 - + + -
1219B TYR* 3.3 36.3 - + + -
1223B PHE* 3.9 22.9 - + - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il